Does this one have a battery disconnect switch? If it does, and it switches two battery+ cables and two + wires, I have seen a bad switch cause poor charging. Put a voltmeter across battery and move the switch around slightly to see if volts go up. Trucks that are left outside a lot get this.

There also is a 50 amp blade fuse for charging on some models. It's located near the valve cover, front.

Also make sure you have a good alt ground and engine ground.